ts_tajima: Calculate Tajima's D for given sets of individuals

In bodkan/slendr: A Simulation Framework for Spatiotemporal Population Genetics

Calculate Tajima's D for given sets of individuals

Description

For a discussion on the difference between "site" and "branch" options of the mode argument, please see the tskit documentation at https://tskit.dev/tskit/docs/stable/stats.html#sec-stats-mode

Usage

ts_tajima(ts, sample_sets, mode = c("site", "branch", "node"), windows = NULL)

Arguments

ts	Tree sequence object of the class slendr_ts
sample_sets	A list (optionally a named list) of character vectors with individual names (one vector per set). If a simple vector is provided, it will be interpreted as as.list(sample_sets), meaning that a given statistic will be calculated for each individual separately.
mode	The mode for the calculation ("sites" or "branch")
windows	Coordinates of breakpoints between windows. The first coordinate (0) and the last coordinate (equal to ts$sequence_length) are added automatically)

Value

For each set of individuals either a single Tajima's D value or a vector of Tajima's D values (one for each window)

Examples

init_env()

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression_slim.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

# load the tree-sequence object from disk
ts <- ts_read(slendr_ts, model) %>% ts_mutate(mutation_rate = 1e-8, random_seed = 42)

# calculate Tajima's D for given sets of individuals in a tree sequence ts
ts_tajima(ts, list(eur = c("EUR_1", "EUR_2", "EUR_3", "EUR_4", "EUR_5"),
                   nea = c("NEA_1", "NEA_2")))

bodkan/slendr documentation built on Dec. 19, 2024, 11:41 p.m.